I have the same issue for 1.7 of my generated LTC in P2POOL which i haven't received into my BTC-E and got same answer from them.
May I know where is those generated amount of LTC in the network?
How is possible ?
You would have to know which block you or the pool solved to get that payout, so you could then go find the coinbase transaction and trace it to your btce address.
This is probably why they tell you not to do what you've done.
Why oh why would you not just have a wallet app running, especially when they tell you NOT to do what you did. Some people's laziness is just astounding.